The gut mycobiome: Implications in piglet health?

Interactions between bacteria and fungi in the gut microbiome can result in altered nutrition, pathogenicity of infection, and host development, making them a crucial component in host health. Associations between the mycobiome and bacteriome in the piglet gut remain unknown. Weaning is a time of significant stress, dietary changes, microbial alterations, and a predisposition to infection. The loss of animal health and growth makes potential microbial interventions of interest to industry. Recent studies have demonstrated the diversity of the microbiome in the gastrointestinal tract of piglets during weaning. Despite these advances, the piglet mycobiota and its contribution to microbiome development remains poorly understood. In this presentation we will review the piglet mycobiome and its interactions with the microbiome and host gastrointestinal (GI) tract. We will highlight our recent data investigating the bacteriome and the mycobiome after weaning in the GI tract organs and feces from 35-d old piglets. The α-diversity and amplicon sequence variants (ASV) counts of the bacteriome increased, proximally to distally, from the stomach to the feces along the GI tract, while the mycobiome α-diversity and ASV counts were highest in the porcine stomach. β-Diversity analyses show distinct clusters based on organ type in the bacteriome and mycobiome, but dispersion remained constant in the mycobiome between organ/fecal sites. Bacteroidetes, Firmicutes, and Epsilonbacteraeota were the most abundant bacterial phyla present and Ascomycota and Basidiomycota were the dominant fungal phyla based on mean taxonomic composition. Potential interactions were found in the lower GI bacteriome and mycobiome with positive correlations between the fungus, Kazachstania, and several bacterial species, including Lactobacillus. Aspergillus demonstrated negative correlations with the short chain fatty acid-producing bacteria Butyricoccus, Subdoligranulum, and Fusicatenibacter. This presentation highlights the distinct colonization dynamics between fungi and bacteria in the GI tract and feces of piglets directly following weaning and the interactions of these microbes in the porcine gut ecosystem.

Key Words: mycobiome, microbiome, weaning, piglet.

Presented at the Symposium on Gut Health in Production of Food Animals 2019 in St. Louis, USA.